[gmx-users] Regarding Umbrella samplling

Justin Lemkul jalemkul at vt.edu
Tue Sep 30 02:43:16 CEST 2014

On 9/29/14 10:09 AM, Sathish Kumar wrote:
> Dear gromacs usres,
>   I have run the umbrella sampling with the help of tutorial of justin....In
> my system rna is binding with gold nanoparticle...to find out the binding
> energy i run the umbrella sampling using the space 0.2 nm and i got total
> 59 configurations, each configuration was run for 5 ns. The profile files
> are shared with the link below.
> https://www.dropbox.com/s/c8tj2rhu620xkim/Slide1.JPG?dl=0
> https://www.dropbox.com/s/745kixwrfvguyyt/Slide2.JPG?dl=0
> In the profile image, i have not got the plateu value, can i take the
> difference between final and starting pmf values for  the binding enrgy.
> Please give suggestions.

You don't have either a plateau or a defined minimum, so I'd say that the 
reaction coordinate is incomplete, either in terms of the sampling within the 
windows or the window setup itself.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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